CoreillCNV_UCSC: Create one track of the genomic positions of CNV in...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/BiofeatureGraphics.R

Description

Create one track of the genomic positions of copy-number variants (CNVs) in chromosomal aberration and inherited disorder cell lines from the NIGMS Human Genetic Cell Repository using the Gviz bioconductor package.

Usage

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CoreillCNV_UCSC(gen, chr, start, end, showId=FALSE)

Arguments

gen

the name of the genome. Data is not currently available for GRCh38 (hg38).

chr

the chromosome of interest

start

the first position in the region of interest (the smallest value)

end

the last position in the region of interest (the largest value)

showId

Show the ID of the genetic elements

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=coriellDelDup

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, COSMIC_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC

Examples

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library("Gviz")
gen <- "hg19"
chrom <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()){
    coreilVariant<-CoreillCNV_UCSC(gen,chrom,start,end)
    plotTracks(coreilVariant, from = start, to =end)
} else {
     data(coreilVarianttrack)
    plotTracks(coreilVariant, from = start, to =end)
}

coMET documentation built on Nov. 23, 2017, 2:05 a.m.